Design of a database to compare genomes

Author

Naresh Pola, Southern Illinois University CarbondaleFollow

Date of Award

8-1-2014

Degree Name

Master of Science

Department

Electrical and Computer Engineering

First Advisor

Nazeih, Botros

Second Advisor

David, Lightfoot

Abstract

Soybean (Glycine max L. Merr.) is one of the largest agricultural crops produced in the world. In recent years the consumption and the production of soybean have both increased. Consequently, the genomics industry has focused on this crop for intense study and analysis. The genome structures of different soybean plants can be better understood by representing their features in a genome database. SoyGD was a soybean genome database which represented the cultivars `Forrest', `Hartwig', `Essex' and `Flyer' genomic feature's in a user-friendly format. The database also provided mapping relationships between genomic features of soybean in general. The use of mapping with micro-satellite and single nucleotide polymorphism markers will provide critical advances in the analysis of crop traits. In this Dissertation SoyGD was modified to present a new Build5 for the Forrest physical map based on the genome sequence. A new set of 1,914 QTL (quantitative trait loci) and also a set of 4,815 new simple sequence repeat (SSRs) markers were added to this browser. Two sets of polymorphic single nucleotide polymorphisms (SNPs) from different genome re-sequencing projects were shown. A set of 10,384 locatable minimum tiling path (MTP) clones were selected from 13,247 BAC clones. They were used to decorate the physical map based on sequence matches by the basic local alignment tool (BLAT). The mapping of QTL, SNPs and SSRs in Forrest and Hartwig are very important tools for breeders and are both economical and technically easy to use. To identify large insertions and deletions insert size distributions of BAC clones were calculated and the respective histogram, density, functions were plotted. Scripting techniques were used to screen the required data from millions of base pairs genomic data and arrange them in a Generic File Format (GFF) to represent in a Genome Database Browser (GBrowser).The study used scripting algorithms to get the minimum tiling path BAC clones and examine expected and observed insert sizes of clones to identify insertions and deletions. BACs were represented in a GBrowser and statistical language was used to plot the insert size distribution of BAC clones.